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-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java240
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java115
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java191
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java91
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java18
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/MadeUpCases.java77
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java269
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestGapMappedToLower.java68
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java33
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java107
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java92
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java38
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java53
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java122
14 files changed, 0 insertions, 1514 deletions
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java b/test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
deleted file mode 100644
index 3f14ec7..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
+++ /dev/null
@@ -1,240 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.semanticweb.owlapi.apibinding.OWLManager;
4import org.semanticweb.owlapi.model.*;
5import org.testng.Assert;
6import org.testng.annotations.Test;
7import uk.ac.ox.cs.pagoda.query.AnswerTuple;
8import uk.ac.ox.cs.pagoda.query.AnswerTuples;
9import uk.ac.ox.cs.pagoda.query.QueryRecord;
10import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
11import uk.ac.ox.cs.pagoda.util.TestUtil;
12
13import java.io.IOException;
14import java.nio.file.Files;
15import java.nio.file.Paths;
16
17import static uk.ac.ox.cs.pagoda.util.TestUtil.getEntityIRI;
18
19public class BugTests {
20
21
22
23 @Test
24 public void minimumCardinalityAxiom2() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
25
26 /*
27 * Build test ontology
28 * */
29
30 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
31 OWLDataFactory factory = manager.getOWLDataFactory();
32 OWLOntology ontology = manager.createOntology();
33
34// OWLClass student = factory.getOWLClass(getEntityIRI("Student"));
35// manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(student));
36// OWLClass course = factory.getOWLClass(getEntityIRI("Course"));
37// manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(course));
38 OWLClass hardWorkingStudent = factory.getOWLClass(getEntityIRI("HardWorkingStudent"));
39 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(hardWorkingStudent));
40 OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
41 OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
42 OWLObjectProperty takesCourse = factory.getOWLObjectProperty(IRI.create(String.format(TestUtil.NS, "takesCourse")));
43 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(takesCourse));
44
45 // Class assertions
46 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(hardWorkingStudent, a)); // HardWorkingStudent(a)
47 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(hardWorkingStudent, b)); // HardWorkingStudent(b)
48
49 // Minimum cardinality axiom
50 manager.addAxiom(ontology,
51 factory.getOWLEquivalentClassesAxiom(hardWorkingStudent,
52 factory.getOWLObjectMinCardinality(3,
53 takesCourse)));
54
55// manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
56
57 /*
58 * Test one query
59 * */
60
61 QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
62 pagoda.loadOntology(ontology);
63 if (pagoda.preprocess()) {
64 String query = "select distinct ?x ?y " +
65 " where { "
66 + " ?x <" + takesCourse.toStringID() + "> _:z . "
67 + " ?y <" + takesCourse.toStringID() + "> _:z " +
68 " }";
69 AnswerTuples answers = pagoda.evaluate(query);
70 int count = 0;
71 for (AnswerTuple ans; answers.isValid(); answers.moveNext()) {
72 ans = answers.getTuple();
73 TestUtil.logInfo(ans);
74 count++;
75 }
76 Assert.assertEquals(count, 2);
77 }
78 pagoda.dispose();
79 }
80
81// @Test
82 public void minimumCardinalityAxiom() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
83
84 /*
85 * Build test ontology
86 * */
87
88 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
89 OWLDataFactory factory = manager.getOWLDataFactory();
90 OWLOntology ontology = manager.createOntology();
91
92 OWLClass student = factory.getOWLClass(getEntityIRI("Student"));
93 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(student));
94 OWLClass course = factory.getOWLClass(getEntityIRI("Course"));
95 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(course));
96 OWLClass hardWorkingStudent = factory.getOWLClass(getEntityIRI("HardWorkingStudent"));
97 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(hardWorkingStudent));
98 OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
99 OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
100 OWLNamedIndividual c1 = factory.getOWLNamedIndividual(getEntityIRI("c1"));
101 OWLNamedIndividual c2 = factory.getOWLNamedIndividual(getEntityIRI("c2"));
102 OWLNamedIndividual c3 = factory.getOWLNamedIndividual(getEntityIRI("c3"));
103 OWLNamedIndividual d1 = factory.getOWLNamedIndividual(getEntityIRI("d1"));
104 OWLNamedIndividual d2 = factory.getOWLNamedIndividual(getEntityIRI("d2"));
105 OWLNamedIndividual d3 = factory.getOWLNamedIndividual(getEntityIRI("d3"));
106 OWLObjectProperty takesCourse = factory.getOWLObjectProperty(IRI.create(String.format(TestUtil.NS, "takesCourse")));
107 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(takesCourse));
108
109 // Class assertions
110 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(student, a)); // Student(a)
111 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(student, b)); // Student(b)
112 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, c1)); // Course(c1)
113 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, c2)); // Course(c2)
114 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, c3)); // Course(c3)
115 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, d1)); // Course(d1)
116 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, d2)); // Course(d2)
117 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, d3)); // Course(d3)
118
119 // Role assertions
120 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, a, c1)); // takesCourse(a,c1)
121 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, a, c2)); // takesCourse(a,c2)
122 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, a, c3)); // takesCourse(a,c3)
123 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, b, d1)); // takesCourse(b,d1)
124 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, b, d2)); // takesCourse(b,d2)
125 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, b, d3)); // takesCourse(b,d3)
126
127 // Minimum cardinality axiom
128 manager.addAxiom(ontology,
129 factory.getOWLEquivalentClassesAxiom(hardWorkingStudent,
130 factory.getOWLObjectMinCardinality(3,
131 takesCourse)));
132
133 manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
134
135 /*
136 * Test one query
137 * */
138
139 QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
140 pagoda.loadOntology(ontology);
141 if (pagoda.preprocess()) {
142 String query = "select distinct ?x ?y " +
143 " where { "
144 + " ?x <" + takesCourse.toStringID() + "> _:z . "
145 + " ?y <" + takesCourse.toStringID() + "> _:z " +
146 " }";
147 AnswerTuples answers = pagoda.evaluate(query);
148 int count = 0;
149 for (AnswerTuple ans; answers.isValid(); answers.moveNext()) {
150 ans = answers.getTuple();
151 TestUtil.logInfo(ans);
152 count++;
153 }
154 Assert.assertEquals(count, 2);
155 }
156 pagoda.dispose();
157 }
158
159 /**
160 * Bug: the relevant ontology is not a subset of the original one.
161 *
162 * @throws OWLOntologyCreationException
163 * @throws IOException
164 * @throws OWLOntologyStorageException
165 */
166// @Test
167 public void rTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
168
169 /*
170 * Build test ontology
171 * */
172
173 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
174 OWLDataFactory factory = manager.getOWLDataFactory();
175 OWLOntology ontology = manager.createOntology();
176
177 OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
178 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
179 OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
180 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
181 OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
182 OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
183 OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
184 OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(TestUtil.NS, "R")));
185 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
186 OWLObjectProperty roleP = factory.getOWLObjectProperty(IRI.create(String.format(TestUtil.NS, "P")));
187 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleP));
188
189 // Class assertions
190 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, a)); // A(a)
191 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, b)); // A(b)
192 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleP, c, a)); // P(c,a)
193
194 // Axioms
195 // subsetOf(A someValuesFrom(R owl:Thing))
196 manager.addAxiom(ontology,
197 factory.getOWLSubClassOfAxiom(classA,
198 factory.getOWLObjectSomeValuesFrom(roleR,
199 factory.getOWLThing())));
200
201 // inverseFunctional(R)
202 manager.addAxiom(ontology,
203 factory.getOWLInverseFunctionalObjectPropertyAxiom(roleR));
204
205 // subsetOf(someValuesFrom(inverseOf(P) owl:thing) B)
206 manager.addAxiom(ontology,
207 factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleP.getInverseProperty(),
208 factory.getOWLThing()),
209 classB));
210 /*
211 * Save the ontology
212 * */
213
214// manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
215
216 /*
217 * Test one query
218 * */
219
220 QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
221 pagoda.loadOntology(ontology);
222 if(pagoda.preprocess()) {
223 String queryStr = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
224 "select distinct ?x" +
225 " where { "
226 + " ?x rdf:type " + classB +
227 " }";
228 QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
229 System.out.println(queryRecord);
230 pagoda.evaluate(queryRecord);
231 AnswerTuples answers = queryRecord.getAnswers();
232 System.out.println("Difficulty: " + queryRecord.getDifficulty());
233 for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
234 ans = answers.getTuple();
235 TestUtil.logInfo(ans);
236 }
237 }
238 pagoda.dispose();
239 }
240}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java b/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java
deleted file mode 100644
index 01e8203..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java
+++ /dev/null
@@ -1,115 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.semanticweb.owlapi.model.OWLOntology;
4import org.testng.annotations.Test;
5import uk.ac.ox.cs.pagoda.owl.OWLHelper;
6import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
7import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner.Type;
8import uk.ac.ox.cs.pagoda.tester.PagodaTester;
9import uk.ac.ox.cs.pagoda.util.TestUtil;
10import uk.ac.ox.cs.pagoda.util.Timer;
11import uk.ac.ox.cs.pagoda.util.Utility;
12
13public class CostEvaluation {
14
15 @Test
16 public void lubm100() {
17 int number = 1;
18 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
19 PagodaTester.main(
20 TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
21 TestUtil.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"),
22 TestUtil.combinePaths(ontoDir, "lubm/queries/test_all_pagoda.sparql")
23 );
24// AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out");
25 }
26
27 public void lubm1000() {
28 int number = 1000;
29 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
30 String[] args = new String[] {
31 TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
32 TestUtil.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"),
33 TestUtil.combinePaths(ontoDir, "lubm/queries/test_all_pagoda.sparql")
34 };
35 OWLOntology ontology = OWLHelper.loadOntology(args[0]);
36 QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true);
37 Timer t = new Timer();
38 reasoner.loadOntology(ontology);
39 reasoner.importData(args[1]);
40 if (!reasoner.preprocess())
41 return ;
42 Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
43
44 reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2]));
45// AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out");
46 }
47
48 @Test
49 public void uobm5() {
50 int number = 1;
51 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
52 String[] args = new String[] {
53 TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
54 TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
55 TestUtil.combinePaths(ontoDir, "uobm/queries/standard_all_pagoda.sparql")
56 };
57 PagodaTester.main(args);
58// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out");
59 }
60
61 public void uobm100() {
62 int number = 200;
63 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
64 String[] args = new String[] {
65 TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
66 TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
67 TestUtil.combinePaths(ontoDir, "uobm/queries/standard_group3_all.sparql")
68 };
69 PagodaTester.main(args);
70// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out");
71 }
72
73 public void uobm500() {
74 int number = 500;
75 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
76 String[] args = new String[] {
77 TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
78 TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
79 TestUtil.combinePaths(ontoDir, "uobm/queries/standard_all_pagoda.sparql")
80 };
81
82 OWLOntology ontology = OWLHelper.loadOntology(args[0]);
83 QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true);
84 Timer t = new Timer();
85 reasoner.loadOntology(ontology);
86 reasoner.importData(args[1]);
87 if (!reasoner.preprocess())
88 return ;
89 Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
90
91 reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2]));
92// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out");
93 }
94
95
96 public static void main(String... args) {
97 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
98 args = new String[] {
99 TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"),
100 TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"),
101 TestUtil.combinePaths(ontoDir, "dbpedia/queries/atomic_ground.sparql")
102 };
103
104 OWLOntology ontology = OWLHelper.loadOntology(args[0]);
105 QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true);
106 Timer t = new Timer();
107 reasoner.loadOntology(ontology);
108 reasoner.importData(args[1]);
109 if (!reasoner.preprocess())
110 return ;
111 Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
112
113 reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2]));
114 }
115}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java
deleted file mode 100644
index 18f6cf9..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java
+++ /dev/null
@@ -1,191 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
5import uk.ac.ox.cs.pagoda.util.TestUtil;
6
7import java.io.IOException;
8
9public class JAIR_PAGOdA {
10
11 public static void main(String... args) {
12 try {
13 new JAIR_PAGOdA().lubm1();
14 } catch(IOException e) {
15 e.printStackTrace();
16 }
17 }
18
19 @Test
20 public void lubm1() throws IOException {
21 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
22 String[] args = new String[] {
23 TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
24 TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"),
25 TestUtil.combinePaths(ontoDir, "lubm/queries/answersCorrectness.sparql")
26 };
27 PagodaTester.main(args);
28 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/pagoda");
29 }
30
31 @Test
32 public void lubm1_conj() throws IOException {
33 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
34 String[] args = new String[] {
35 TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
36 TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"),
37 TestUtil.combinePaths(ontoDir, "lubm/queries/test_pellet.sparql")
38 };
39 PagodaTester.main(args);
40 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/pagoda_conj");
41 }
42
43 @Test
44 public void lubm1_rolledUp() throws IOException {
45 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
46 PagodaTester.main(
47 "/home/yzhou/backup/20141212/univ-bench-queries.owl",
48 TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"),
49 TestUtil.combinePaths(ontoDir, "lubm/queries/atomic_lubm.sparql")
50 );
51 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/pagoda_rolledUp");
52 }
53
54 @Test
55 public void uobm1() throws IOException {
56 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
57 String[] args = new String[] {
58 TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
59 TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"),
60 TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql")
61 };
62 PagodaTester.main(args);
63 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/pagoda");
64 }
65
66 @Test
67 public void uobm1_conj() throws IOException {
68 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
69 String[] args = new String[] {
70 TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
71 TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"),
72 TestUtil.combinePaths(ontoDir, "uobm/queries/standard_pellet.sparql")
73 };
74 PagodaTester.main(args);
75 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/pagoda_conj");
76 }
77
78 @Test
79 public void uobm1_rolledUp() {
80 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
81 String[] args = new String[] {
82 "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl",
83 TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"),
84 TestUtil.combinePaths(ontoDir, "uobm/queries/atomic_uobm.sparql")
85 };
86 PagodaTester.main(args);
87// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/pagoda_rolledUp");
88 }
89
90 @Test
91 public void fly() {
92 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
93 String[] args = new String[] {
94 TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"),
95 null,
96 TestUtil.combinePaths(ontoDir, "fly/queries/fly_pellet.sparql")
97 };
98 PagodaTester.main(args);
99// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/fly/pagoda");
100 }
101
102 @Test
103 public void fly_conj() throws IOException {
104 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
105 String[] args = new String[] {
106 TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"),
107 null,
108 TestUtil.combinePaths(ontoDir, "fly/queries/fly_pellet.sparql")
109 };
110 PagodaTester.main(args);
111 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/fly/pagoda_conj");
112 }
113
114 public void fly_rolledUp() {
115 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
116 PagodaTester.main(
117// TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
118 TestUtil.combinePaths(ontoDir, "fly/fly-all-in-one_rolledUp.owl"),
119 null,
120 TestUtil.combinePaths(ontoDir, "fly/queries/fly_atomic.sparql")
121 );
122// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/fly/pagoda_rolledUp");
123 }
124
125 public void dbpedia() {
126 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
127 PagodaTester.main(
128 TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"),
129 TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"),
130 TestUtil.combinePaths(ontoDir, "dbpedia/queries/atomic_ground.sparql"),
131 "dbpedia.ans"
132 );
133
134// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/dbpedia/pagoda");
135 }
136
137 public void npd() {
138 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
139 PagodaTester.main(
140 TestUtil.combinePaths(ontoDir, "npd/npd-all-minus-datatype.owl"),
141 TestUtil.combinePaths(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"),
142 TestUtil.combinePaths(ontoDir, "npd/queries/atomic_ground.sparql")
143 , "npd.ans"
144 );
145
146// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/npd/pagoda");
147 }
148
149 public void reactome() throws IOException {
150 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
151 PagodaTester.main(
152 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"),
153 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl"),
154// null,
155// TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/atomic_ground.sparql")
156 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/example.sparql")
157 , "pagoda_reactome.ans"
158 );
159 TestUtil.copyFile("log4j.log", "output/jair/pagoda_reactome.example");
160
161// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/reactome/pagoda_10p");
162 }
163
164 public void chembl() throws IOException {
165 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
166 PagodaTester.main(
167 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"),
168 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/graph sampling/sample_1.nt"),
169// TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql")
170 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/example.sparql")
171 , "pagoda_chembl.ans"
172 );
173 TestUtil.copyFile("log4j.log", "output/jair/pagoda_chembl.example");
174// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/chembl/pagoda_1p");
175 }
176
177 public void uniprot() throws IOException {
178 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
179 PagodaTester.main(
180 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat-processed.owl"),
181 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/graph sampling/sample_1.nt"),
182// null,
183// TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql")
184 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/example.sparql")
185 , "pagoda_uniprot.ans"
186 );
187 TestUtil.copyFile("log4j.log", "output/jair/pagoda_uniprot.example");
188// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uniprot/pagoda_1p");
189 }
190
191}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java
deleted file mode 100644
index 01f3568..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java
+++ /dev/null
@@ -1,91 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
5import uk.ac.ox.cs.pagoda.util.PagodaProperties;
6import uk.ac.ox.cs.pagoda.util.TestUtil;
7
8import java.io.IOException;
9
10public class JAIR_Scalability {
11
12 private static final String date = "_0123";
13
14 public static void main(String... args) throws IOException {
15 PagodaProperties.shellModeDefault = true;
16 new JAIR_Scalability().testUniProt(50, false);
17 }
18
19 @Test
20 public void reactome() throws IOException {
21 testReactome(10, false);
22 }
23
24 @Test
25 public void chembl() throws IOException {
26 testChEMBL(1, false);
27 }
28
29 @Test
30 public void uniprot() throws IOException {
31 testUniProt(1, false);
32 }
33
34 public void testReactome(int percentage, boolean save) throws IOException {
35 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
36 String[] args = new String[] {
37 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"),
38 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/simplifed_sample_" + percentage + ".ttl"),
39 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/answersCorrectness.sparql")
40 , "reactome.ans"
41 };
42 if (percentage == 10)
43 args[1] = args[1].replace("simplifed", "reactome");
44
45 PagodaTester.main(args);
46 if (save)
47 TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/reactome/pagoda_" + percentage + "p" + date);
48 }
49
50 public void testChEMBL(int percentage, boolean save) throws IOException {
51 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
52 String[] args = new String[] {
53 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"),
54 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/sample_" + percentage + ".nt"),
55// TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql")
56 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/answersCorrectness.sparql")
57 , "chembl.ans"
58 };
59 if (percentage == 1 || percentage == 10 || percentage == 50)
60 args[1] = args[1].replace("chembl", "chembl/graph sampling");
61 else
62 if (percentage == 100)
63 args[1] = "/home/yzhou/RDFData/ChEMBL/facts/ChEMBL.ttl";
64
65 PagodaTester.main(args);
66 if (save)
67 TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/chembl/pagoda_" + percentage + "p" + date);
68 }
69
70 public void testUniProt(int percentage, boolean save) throws IOException {
71 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
72 String[] args = new String[] {
73 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat-processed.owl"),
74 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/sample_" + percentage + ".nt"),
75// TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql")
76 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/answersCorrectness.sparql")
77 , "uniprot.ans"
78 };
79
80 if (percentage == 1 || percentage == 10 || percentage == 50)
81 args[1] = args[1].replace("uniprot", "uniprot/graph sampling");
82 else
83 if (percentage == 100)
84 args[1] = "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/data/uniprot_cleaned.nt";
85
86 PagodaTester.main(args);
87 if (save)
88 TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uniprot/pagoda_" + percentage + "p" + date);
89 }
90
91}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java b/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java
deleted file mode 100644
index 3551b9b..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java
+++ /dev/null
@@ -1,18 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4
5import java.io.IOException;
6
7@Deprecated
8public class LightEvaluation {
9
10 @Test
11 public void evaluation() throws IOException {
12 new TestPagodaUOBM().answersCorrectness(1);
13 new TestPagodaLUBM().answersCorrectness(100);
14// new TestPagodaFLY().answersCorrectness();
15 new TestPagodaDBPedia().answersCorrectness();
16 new TestPagodaNPD().testNPDwithoutDataType();
17 }
18}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/MadeUpCases.java b/test/uk/ac/ox/cs/pagoda/global_tests/MadeUpCases.java
deleted file mode 100644
index 3d154cb..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/MadeUpCases.java
+++ /dev/null
@@ -1,77 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.semanticweb.owlapi.apibinding.OWLManager;
4import org.semanticweb.owlapi.model.*;
5import org.testng.Assert;
6import org.testng.annotations.Test;
7import uk.ac.ox.cs.pagoda.query.AnswerTuple;
8import uk.ac.ox.cs.pagoda.query.AnswerTuples;
9import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
10import uk.ac.ox.cs.pagoda.util.TestUtil;
11
12import java.io.IOException;
13
14import static uk.ac.ox.cs.pagoda.util.TestUtil.getEntityIRI;
15
16public class MadeUpCases {
17
18 @Test(groups = {"existential"})
19 public void someTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
20
21 /*
22 * Build test ontology
23 * */
24
25 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
26 OWLDataFactory factory = manager.getOWLDataFactory();
27 OWLOntology ontology = manager.createOntology();
28
29 OWLClass A1 = factory.getOWLClass(getEntityIRI("A1"));
30 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A1));
31 OWLClass A2 = factory.getOWLClass(getEntityIRI("A2"));
32 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A2));
33 OWLClass A3 = factory.getOWLClass(getEntityIRI("A3"));
34 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A3));
35 OWLClass A4 = factory.getOWLClass(getEntityIRI("A4"));
36 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A4));
37 OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
38 OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
39 OWLObjectProperty R = factory.getOWLObjectProperty(IRI.create(String.format(TestUtil.NS, "R")));
40 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(R));
41
42 // Class assertions
43 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(A1, a));
44 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(A1, b));
45
46 // Minimum cardinality axiom
47 manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A1, factory.getOWLObjectSomeValuesFrom(R, A2)));
48 manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A2, factory.getOWLObjectSomeValuesFrom(R, A3)));
49 manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A3, factory.getOWLObjectSomeValuesFrom(R, A4)));
50 manager.addAxiom(ontology, factory.getOWLTransitiveObjectPropertyAxiom(R));
51
52// manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
53
54 /*
55 * Test one query
56 * */
57
58 QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
59 pagoda.loadOntology(ontology);
60 if (pagoda.preprocess()) {
61 String query = "select distinct ?x ?y " +
62 " where { "
63 + " ?x <" + R.toStringID() + "> _:z . "
64 + " ?y <" + R.toStringID() + "> _:z " +
65 " }";
66 AnswerTuples answers = pagoda.evaluate(query);
67 int count = 0;
68 for (AnswerTuple ans; answers.isValid(); answers.moveNext()) {
69 ans = answers.getTuple();
70 TestUtil.logInfo(ans);
71 count++;
72 }
73 Assert.assertEquals(count, 2);
74 }
75 pagoda.dispose();
76 }
77}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java b/test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java
deleted file mode 100644
index 2fc682b..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java
+++ /dev/null
@@ -1,269 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.semanticweb.owlapi.apibinding.OWLManager;
4import org.semanticweb.owlapi.model.*;
5import org.testng.Assert;
6import org.testng.annotations.Test;
7import uk.ac.ox.cs.pagoda.query.AnswerTuple;
8import uk.ac.ox.cs.pagoda.query.AnswerTuples;
9import uk.ac.ox.cs.pagoda.query.QueryRecord;
10import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
11import uk.ac.ox.cs.pagoda.util.TestUtil;
12
13import java.io.IOException;
14import java.nio.file.Files;
15import java.nio.file.Paths;
16
17public class SkolemisationTests {
18
19 public static final String NS = "http://example.org/test#%s";
20
21 private IRI getEntityIRI(String name) {
22 return IRI.create(String.format(NS, name));
23 }
24
25// @Test
26 public void commonSuccessorTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
27
28 /*
29 * Build test ontology
30 * */
31
32 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
33 OWLDataFactory factory = manager.getOWLDataFactory();
34 OWLOntology ontology = manager.createOntology();
35
36 OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
37 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
38 OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
39 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
40 OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
41 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
42 OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
43 OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
44 OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
45 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
46
47 // Class assertions
48 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, c)); // A(c)
49 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, d)); // A(d)
50
51 // Minimum cardinality axiom
52 manager.addAxiom(ontology,
53 factory.getOWLSubClassOfAxiom(classA,
54 factory.getOWLObjectUnionOf(
55 factory.getOWLObjectSomeValuesFrom(roleR, classB),
56 factory.getOWLObjectSomeValuesFrom(roleR, classC))));
57
58 /*
59 * Save the ontology
60 * */
61
62// manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
63
64 /*
65 * Test one query
66 * */
67
68 QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
69 pagoda.loadOntology(ontology);
70 if(pagoda.preprocess()) {
71 String queryStr = "select distinct ?x ?y " +
72 " where { "
73 + " ?x <" + roleR.toStringID() + "> _:z . "
74 + " ?y <" + roleR.toStringID() + "> _:z " +
75 " }";
76 QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
77 pagoda.evaluate(queryRecord);
78 AnswerTuples answers = queryRecord.getAnswers();
79 System.out.println("Difficulty: " + queryRecord.getDifficulty());
80 int count = 0;
81 for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
82 ans = answers.getTuple();
83 TestUtil.logInfo(ans);
84 count++;
85 }
86 Assert.assertEquals(count, 2);
87 }
88 pagoda.dispose();
89 }
90
91// @Test
92 public void yTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
93
94 /*
95 * Build test ontology
96 * */
97
98 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
99 OWLDataFactory factory = manager.getOWLDataFactory();
100 OWLOntology ontology = manager.createOntology();
101
102 OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
103 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
104 OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
105 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
106 OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
107 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
108 OWLClass classD = factory.getOWLClass(getEntityIRI("D"));
109 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classD));
110 OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
111 OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
112 OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
113 OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
114 OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
115 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
116 OWLObjectProperty roleS = factory.getOWLObjectProperty(IRI.create(String.format(NS, "S")));
117 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleS));
118 OWLObjectProperty roleP = factory.getOWLObjectProperty(IRI.create(String.format(NS, "P")));
119 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleP));
120
121 // Class assertions
122 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classD, a)); // D(a)
123 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classD, b)); // D(b)
124 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleS, c, a)); // S(c,a)
125 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleP, d, b)); // P(d,b)
126
127 // Axioms
128 // subsetOf(D someValuesFrom(R owl:Thing))
129 manager.addAxiom(ontology,
130 factory.getOWLSubClassOfAxiom(classD,
131 factory.getOWLObjectSomeValuesFrom(roleR,
132 factory.getOWLThing())));
133 // subsetOf(someValuesFrom(inverseOf(S) owl:Thing) allValuesFrom(R A))
134 manager.addAxiom(ontology,
135 factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleS.getInverseProperty(),
136 factory.getOWLThing()),
137 factory.getOWLObjectAllValuesFrom(roleR, classA)));
138 // subsetOf(someValuesFrom(inverseOf(P) owl:Thing) B)
139 manager.addAxiom(ontology,
140 factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleP.getInverseProperty(),
141 factory.getOWLThing()),
142 classB));
143 // subsetOf(someValuesFrom(R A) C)
144 manager.addAxiom(ontology,
145 factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleR, classA), classC));
146
147 /*
148 * Save the ontology
149 * */
150
151 manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
152
153 /*
154 * Test one query
155 * */
156
157 QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
158 pagoda.loadOntology(ontology);
159 if(pagoda.preprocess()) {
160 String queryStr = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
161 "select distinct ?x" +
162 " where { "
163// + " ?x rdf:type " + classB + " ."
164// + " ?x " + roleR + " "+ "_:y . "
165 + " ?x rdf:type " + classC +
166 " }";
167 QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
168 System.out.println(queryRecord);
169 pagoda.evaluate(queryRecord);
170 AnswerTuples answers = queryRecord.getAnswers();
171 System.out.println("Difficulty: " + queryRecord.getDifficulty());
172 int count = 0;
173 for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
174 ans = answers.getTuple();
175 TestUtil.logInfo(ans);
176 count++;
177 }
178// Assert.assertEquals(count, 1);
179 }
180 pagoda.dispose();
181 }
182
183 @Test
184 public void rTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
185
186 /*
187 * Build test ontology
188 * */
189
190 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
191 OWLDataFactory factory = manager.getOWLDataFactory();
192 OWLOntology ontology = manager.createOntology();
193
194 OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
195 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
196 OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
197 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
198// OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
199// manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
200// OWLClass classD = factory.getOWLClass(getEntityIRI("D"));
201// manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classD));
202 OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
203 OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
204 OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
205// OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
206 OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
207 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
208// OWLObjectProperty roleF = factory.getOWLObjectProperty(IRI.create(String.format(NS, "F")));
209// manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleF));
210 OWLObjectProperty roleP = factory.getOWLObjectProperty(IRI.create(String.format(NS, "P")));
211 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleP));
212// OWLObjectProperty roleL = factory.getOWLObjectProperty(IRI.create(String.format(NS, "L")));
213// manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleL));
214
215 // Class assertions
216 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, a)); // A(a)
217 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, b)); // A(b)
218 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleP, c, a)); // P(c,a)
219
220 // Axioms
221 // subsetOf(A someValuesFrom(R owl:Thing))
222 manager.addAxiom(ontology,
223 factory.getOWLSubClassOfAxiom(classA,
224 factory.getOWLObjectSomeValuesFrom(roleR,
225 factory.getOWLThing())));
226
227 // inverseFunctional(R)
228 manager.addAxiom(ontology,
229 factory.getOWLInverseFunctionalObjectPropertyAxiom(roleR));
230
231 // subsetOf(someValuesFrom(inverseOf(P) owl:thing) B)
232 manager.addAxiom(ontology,
233 factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleP.getInverseProperty(),
234 factory.getOWLThing()),
235 classB));
236 /*
237 * Save the ontology
238 * */
239
240 manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
241
242 /*
243 * Test one query
244 * */
245
246 QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
247 pagoda.loadOntology(ontology);
248 if(pagoda.preprocess()) {
249 String queryStr = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
250 "select distinct ?x" +
251 " where { "
252 + " ?x rdf:type " + classB +
253 " }";
254 QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
255 System.out.println(queryRecord);
256 pagoda.evaluate(queryRecord);
257 AnswerTuples answers = queryRecord.getAnswers();
258 System.out.println("Difficulty: " + queryRecord.getDifficulty());
259 int count = 0;
260 for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
261 ans = answers.getTuple();
262 TestUtil.logInfo(ans);
263 count++;
264 }
265// Assert.assertEquals(count, 1);
266 }
267 pagoda.dispose();
268 }
269}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestGapMappedToLower.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestGapMappedToLower.java
deleted file mode 100644
index 4b1ec6d..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestGapMappedToLower.java
+++ /dev/null
@@ -1,68 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import junit.framework.Assert;
4import org.semanticweb.owlapi.apibinding.OWLManager;
5import org.semanticweb.owlapi.model.*;
6import org.testng.annotations.Test;
7import uk.ac.ox.cs.pagoda.query.AnswerTuple;
8import uk.ac.ox.cs.pagoda.query.AnswerTuples;
9import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
10import uk.ac.ox.cs.pagoda.util.Namespace;
11
12public class TestGapMappedToLower {
13
14 public static final String ns = "http://example.org/test#%s";
15
16 public IRI getEntityIRI(String name) {
17 return IRI.create(String.format(ns, name));
18 }
19
20 @Test
21 public void test() throws OWLOntologyCreationException {
22 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
23 OWLDataFactory factory = manager.getOWLDataFactory();
24 OWLOntology ontology = manager.createOntology();
25 OWLClass A = factory.getOWLClass(getEntityIRI("A"));
26 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A));
27 OWLClass B = factory.getOWLClass(getEntityIRI("B"));
28 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(B));
29 OWLClass C = factory.getOWLClass(getEntityIRI("C"));
30 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(C));
31 OWLClass A1 = factory.getOWLClass(getEntityIRI("A1"));
32 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A1));
33 OWLClass A2 = factory.getOWLClass(getEntityIRI("A2"));
34 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A2));
35 OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
36 OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
37 OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
38 OWLObjectProperty r = factory.getOWLObjectProperty(IRI.create(String.format(ns, "r")));
39 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(r));
40
41 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(A, a)); // A(a)
42 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(B, b)); // B(b)
43 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(C, c)); // C(c)
44 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(r, a, b)); // r(a,b)
45 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(r, a, c)); // r(a,c)
46 manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A, factory.getOWLObjectUnionOf(A1, A2))); // A \sqsubseteq A1 \sqcup A2
47 manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A1, factory.getOWLObjectMaxCardinality(1, r))); // A1 \sqsubseteq \leq 1 r.\top
48 manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A2, factory.getOWLObjectMaxCardinality(1, r))); // A2 \sqsubseteq \leq 1 r.\top
49
50 QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
51 pagoda.loadOntology(ontology);
52 if (pagoda.preprocess()) {
53 String sparql = "select ?x where { "
54 + "?x <" + r.toStringID() + "> ?y . "
55 + "?y " + Namespace.RDF_TYPE_QUOTED + " <" + B.toStringID() + "> . "
56 + "?y " + Namespace.RDF_TYPE_QUOTED + " <" + C.toStringID() + "> . } ";
57 AnswerTuples rs = pagoda.evaluate(sparql);
58 int count = 0;
59 for (AnswerTuple ans; rs.isValid(); rs.moveNext()) {
60 ans = rs.getTuple();
61 System.out.println(ans.getGroundTerm(0));
62 ++count;
63 }
64 Assert.assertEquals(1, count);
65 }
66 }
67
68}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java
deleted file mode 100644
index 3642147..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java
+++ /dev/null
@@ -1,33 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.Pagoda;
5import uk.ac.ox.cs.pagoda.util.TestUtil;
6
7import java.io.IOException;
8import java.nio.file.Paths;
9
10public class TestPagodaDBPedia {
11
12 public static final String ANSWER_PATH = "~/TestPagodaDEBPedia.json";
13
14 @Test
15 public void just_execute() throws IOException {
16 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
17 Pagoda pagoda = Pagoda.builder()
18 .ontology(Paths.get(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"))
19 .data(Paths.get(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"))
20 .query(Paths.get(ontoDir, "dbpedia/atomic.sparql"))
21 .answer(ANSWER_PATH)
22 .classify(true)
23 .hermit(true)
24 .build();
25 pagoda.run();
26 }
27
28 @Test
29 public void answersCorrectness() {
30 // TODO implement
31 }
32
33}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
deleted file mode 100644
index 3eb956f..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
+++ /dev/null
@@ -1,107 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.Pagoda;
5import uk.ac.ox.cs.pagoda.query.CheckAnswers;
6import uk.ac.ox.cs.pagoda.util.PagodaProperties;
7import uk.ac.ox.cs.pagoda.util.TestUtil;
8import uk.ac.ox.cs.pagoda.util.Timer;
9
10import java.io.File;
11import java.io.IOException;
12import java.nio.file.Path;
13import java.nio.file.Paths;
14
15public class TestPagodaFLY {
16
17 // @Test(groups = {"light"})
18 public void answersCorrectness_withGJFC() throws IOException {
19 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
20 Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
21 new File(answers.toString()).deleteOnExit();
22 Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-fly-with-GJ-FC-individuals.json");
23
24 Pagoda pagoda = Pagoda.builder()
25 .ontology(Paths.get(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"))
26 .query(Paths.get(ontoDir, "fly/queries/fly.sparql"))
27 .answer(answers)
28 .classify(false)
29 .build();
30
31 pagoda.run();
32 CheckAnswers.assertSameAnswers(answers, givenAnswers);
33 }
34
35 @Test(groups = {"light", "correctness"})
36 public void answersCorrectness_rolledUp() throws IOException {
37 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
38 Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
39 new File(answers.toString()).deleteOnExit();
40 Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-fly-rolledup.json");
41
42 Pagoda pagoda = Pagoda.builder()
43 .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
44 .query(Paths.get(ontoDir, "fly/queries/fly_rolledUp.sparql"))
45 .answer(answers)
46// .answer(Paths.get("/home/alessandro/Desktop/answers.json"))
47 .classify(false)
48 .build();
49
50 pagoda.run();
51 CheckAnswers.assertSameAnswers(answers, givenAnswers);
52 }
53
54 @Test(groups = {"light", "justExecute", "nonOriginal", "existential"})
55 public void justExecute_newQueries() throws IOException {
56 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
57
58 Pagoda.builder()
59// .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
60 .ontology(Paths.get(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"))
61// .query(Paths.get(ontoDir, "fly/queries/fly_rolledUp.sparql"))
62// .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql"))
63 .query("/home/alessandro/Desktop/query-8.sparql")
64// .answer(Paths.get("/home/alessandro/Desktop/answers.json"))
65 .classify(false)
66 .hermit(true)
67 .skolemDepth(3)
68 .skolem(PagodaProperties.SkolemUpperBoundOptions.BEFORE_SUMMARISATION)
69 .build()
70 .run();
71 }
72
73 @Test(groups = {"comparison"})
74 public void compare_newQueries() throws IOException {
75 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
76
77 Timer timer = new Timer();
78 Pagoda.builder()
79 .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
80 .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql"))
81 .classify(false)
82 .hermit(true)
83 .skolem(PagodaProperties.SkolemUpperBoundOptions.AFTER_SUMMARISATION) // <----<< Skolem upper bound is ENABLED <<<
84 .build()
85 .run();
86 double t1 = timer.duration();
87
88 timer.reset();
89
90 Pagoda.builder()
91 .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
92 .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql"))
93 .classify(false)
94 .hermit(true)
95 .skolem(PagodaProperties.SkolemUpperBoundOptions.DISABLED) // <----<< Skolem upper bound is DISABLED <<<
96 .build()
97 .run();
98 double t2 = timer.duration();
99
100 if(t1 < t2)
101 TestUtil.logInfo(
102 "Overall reasoning with Skolem upper bound was " + (int) (t2 / t1 * 100 - 100) + "x faster!");
103 else
104 TestUtil.logInfo(
105 "Overall reasoning with Skolem upper bound was " + (int) (t1 / t2 * 100 - 100) + "x slower...");
106 }
107}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
deleted file mode 100644
index 019fafa..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
+++ /dev/null
@@ -1,92 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.Pagoda;
5import uk.ac.ox.cs.pagoda.query.CheckAnswers;
6import uk.ac.ox.cs.pagoda.util.TestUtil;
7
8import java.io.File;
9import java.io.IOException;
10import java.nio.file.Path;
11import java.nio.file.Paths;
12
13public class TestPagodaLUBM {
14
15 public void answersCorrectness(int number) throws IOException {
16 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
17 Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
18 new File(answers.toString()).deleteOnExit();
19 Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-lubm" + number + ".json");
20
21 Pagoda pagoda = Pagoda.builder()
22 .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl"))
23 .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"))
24 .query(Paths.get(ontoDir, "lubm/queries/test.sparql"))
25 .answer(answers)
26 .build();
27
28 pagoda.run();
29 CheckAnswers.assertSameAnswers(answers, givenAnswers);
30 }
31
32 @Test(groups = {"light", "correctness"})
33 public void answersCorrectness_1() throws IOException {
34 answersCorrectness(1);
35 }
36
37 public void justExecute_sygenia(int number) throws IOException {
38 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
39// Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
40// new File(answers.toString()).deleteOnExit();
41// Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-lubm" + number + ".json");
42
43 Pagoda pagoda = Pagoda.builder()
44 .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl"))
45 .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"))
46 .query(Paths.get(ontoDir, "lubm/queries/lubm_sygenia.sparql"))
47// .answer(answers)
48 .build();
49
50 pagoda.run();
51// CheckAnswers.assertSameAnswers(answers, givenAnswers);
52 }
53
54 @Test(groups = {"sygenia"})
55 public void justExecute_sygenia_1() throws IOException {
56 justExecute_sygenia(1);
57 }
58
59 public void justExecute_sygenia_allBlanks(int number) throws IOException {
60 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
61// Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
62// new File(answers.toString()).deleteOnExit();
63// Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-lubm" + number + ".json");
64
65 Pagoda pagoda = Pagoda.builder()
66 .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl"))
67 .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"))
68 .query(Paths.get(ontoDir, "lubm/queries/lubm_sygenia_all-blanks.sparql"))
69// .answer(answers)
70 .build();
71
72 pagoda.run();
73// CheckAnswers.assertSameAnswers(answers, givenAnswers);
74 }
75
76 @Test(groups = {"sygenia"})
77 public void justExecute_sygenia_1_allBlanks() throws IOException {
78 justExecute_sygenia_allBlanks(1);
79 }
80
81 @Test(groups = {"existential"})
82 public void justExecute_feier() throws IOException {
83 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
84
85 Pagoda.builder()
86 .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl"))
87 .data(Paths.get(ontoDir, "lubm/data/lubm1.ttl"))
88 .query(Paths.get(ontoDir, "lubm/queries/queries_from_rules.sparql"))
89 .build()
90 .run();
91 }
92}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java
deleted file mode 100644
index 939ee6e..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java
+++ /dev/null
@@ -1,38 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.Pagoda;
5import uk.ac.ox.cs.pagoda.util.TestUtil;
6
7import java.io.IOException;
8import java.nio.file.Paths;
9
10public class TestPagodaNPD {
11
12 public static final String ANSWER_PATH = "~/PagodaNPDWithoutDatatype.json";
13
14 @Test
15 public void justExecuteNPDWithoutDataType() {
16 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
17 Pagoda pagoda = Pagoda.builder()
18 .ontology(Paths.get(ontoDir, "npd/npd-all-minus-datatype.owl"))
19 .data(Paths.get(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"))
20 .query(Paths.get(ontoDir, "npd/queries/atomic.sparql"))
21 .answer(ANSWER_PATH)
22 .classify(true)
23 .hermit(true)
24 .build();
25 pagoda.run();
26 }
27
28 @Test
29 public void testNPDwithoutDataType() throws IOException {
30 // TODO implement
31 }
32
33 @Test
34 public void testNPD() throws IOException {
35 // TODO implement
36 }
37
38}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
deleted file mode 100644
index 8a8a596..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
+++ /dev/null
@@ -1,53 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.Pagoda;
5import uk.ac.ox.cs.pagoda.util.TestUtil;
6
7import java.io.IOException;
8import java.nio.file.Paths;
9
10public class TestPagodaReactome {
11
12 @Test(groups = {"justExecute"})
13 public void justExecute() throws IOException {
14 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
15
16 Pagoda.builder()
17 .ontology(Paths.get(ontoDir, "reactome/biopax-level3-processed.owl"))
18 .data(Paths.get(ontoDir, "reactome/data/sample_10.ttl"))
19 .query(Paths.get(ontoDir, "reactome/test.sparql"))
20 .classify(true)
21 .hermit(true)
22 .build()
23 .run();
24 }
25
26 @Test(groups = {"sygenia"})
27 public void justExecute_sygenia() throws IOException {
28 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
29
30 Pagoda.builder()
31 .ontology(Paths.get(ontoDir, "reactome/biopax-level3-processed.owl"))
32 .data(Paths.get(ontoDir, "reactome/data/sample_10.ttl"))
33 .query(Paths.get(ontoDir, "reactome/reactome_sygenia_queries.sparql"))
34 .classify(true)
35 .hermit(true)
36 .build()
37 .run();
38 }
39
40 @Test(groups = {"existential"})
41 public void justExecute_existential() throws IOException {
42 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
43
44 Pagoda.builder()
45 .ontology(Paths.get(ontoDir, "reactome/biopax-level3-processed.owl"))
46 .data(Paths.get(ontoDir, "reactome/data/sample_10.ttl"))
47 .query(Paths.get(ontoDir, "reactome/existential_queries.sparql"))
48// .query(Paths.get(ontoDir, "reactome/Queries_by_Feier-et-al.sparql"))
49 .build()
50 .run();
51 }
52
53}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
deleted file mode 100644
index 4dae223..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
+++ /dev/null
@@ -1,122 +0,0 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.DataProvider;
4import org.testng.annotations.Test;
5import uk.ac.ox.cs.pagoda.Pagoda;
6import uk.ac.ox.cs.pagoda.query.CheckAnswers;
7import uk.ac.ox.cs.pagoda.util.TestUtil;
8
9import java.io.File;
10import java.io.IOException;
11import java.nio.file.Path;
12import java.nio.file.Paths;
13
14public class TestPagodaUOBM {
15
16 private static final int N_1 = 1;
17 private static final int N_2 = 4;
18
19 @DataProvider(name = "UOBMNumbers")
20 private static Object[][] UOBMNumbers() {
21 Integer[][] integers = new Integer[N_2 - N_1 + 1][1];
22 for(int i = 0; i < N_2 - N_1 + 1; i++)
23 integers[i][0] = N_1 + i;
24 return integers;
25 }
26
27 @Test(groups = {"light", "correctness"})
28 public void answersCorrectness_1() throws IOException {
29 answersCorrectness(1);
30 }
31
32 @Test(groups = {"heavy", "correctness"}, dataProvider = "UOBMNumbers")
33 public void answersCorrectness(int number) throws IOException {
34 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
35 Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
36 new File(answers.toString()).deleteOnExit();
37 Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-uobm" + number + ".json");
38
39 Pagoda pagoda = Pagoda.builder()
40 .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
41 .data(Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"))
42 .query(Paths.get(ontoDir, "uobm/queries/test.sparql"))
43 .answer(answers)
44 .build();
45
46 pagoda.run();
47 CheckAnswers.assertSameAnswers(answers, givenAnswers);
48 }
49
50 @Test(groups = {"sygenia"})
51 public void answersCorrectness_sygenia_1() throws IOException {
52 answersCorrectness_sygenia(1);
53 }
54
55 @Test(groups = {"heavy",}, dataProvider = "UOBMNumbers")
56 public void answersCorrectness_sygenia(int number) throws IOException {
57 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
58// Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
59// new File(answers.toString()).deleteOnExit();
60// Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-uobm" + number + ".json");
61
62 Pagoda pagoda = Pagoda.builder()
63 .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
64 .data(Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"))
65 .query(Paths.get(ontoDir, "uobm/queries/uobm_sygenia.sparql"))
66 .build();
67
68 pagoda.run();
69 }
70
71 @Test(groups = {"sygenia"})
72 public void answersCorrectness_sygenia_allBlanks_1() throws IOException {
73 answersCorrectness_sygenia(1);
74 }
75
76 @Test(groups = {"heavy"}, dataProvider = "UOBMNumbers")
77 public void answersCorrectness_sygenia_allBlanks(int number) throws IOException {
78 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
79
80 Pagoda.builder()
81 .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
82 .data(Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"))
83 .query(Paths.get(ontoDir, "uobm/queries/uobm_sygenia_all-blanks.sparql"))
84 .build()
85 .run();
86 }
87
88 @Test(groups = {"justExecute", "heavy", "nonOriginal", "existential"})
89 public void justExecute_modifiedUOBM() throws IOException {
90 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
91
92 Pagoda.builder()
93 .ontology(Paths.get(ontoDir, "uobm_modified/univ-bench-dl-modified.owl"))
94 .data(Paths.get(ontoDir, "uobm_modified/data/uobm1.ttl"))
95 .query(Paths.get(ontoDir, "uobm_modified/queries/additional_queries.sparql"))
96 .build()
97 .run();
98 }
99
100 @Test(groups = {"justExecute"})
101 public void justExecute_additionalQueries() throws IOException {
102 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
103
104 Pagoda.builder()
105 .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
106 .data(Paths.get(ontoDir, "uobm/data/uobm1.ttl"))
107 .query(Paths.get(ontoDir, "uobm/queries/additional_queries.sparql"))
108 .build()
109 .run();
110 }
111
112 @Test(groups = {"justExecute", "UOBM50"})
113 public void justExecuteUOBM_50() throws IOException {
114 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
115 Pagoda.builder()
116 .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
117 .data(Paths.get(ontoDir, "uobm/data/uobm50.ttl"))
118 .query(Paths.get(ontoDir, "uobm/queries/test.sparql"))
119 .build()
120 .run();
121 }
122}
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-05 20:46:45 +0000